Spectroscopic studies on two-iron ferredoxins

1974 ◽  
Vol 7 (4) ◽  
pp. 443-504 ◽  
Author(s):  
R. H. Sands ◽  
W. R. Dunham
Keyword(s):  
High Spin ◽  
Active Site ◽  
Active Sites ◽  
Spectroscopic Studies ◽  
Transport Proteins ◽  
Distorted Tetrahedron ◽  
X Ray ◽  
Iron Proteins ◽  
Electron Transport Proteins ◽  
Reduced State

The application of magnetic resonance techniques to biological systems has permitted a detailed study of the nature of the active sites of many proteins that had not been possible previously. Among these is the whole class of iron—sulphur proteins which have been implicated as electron transport proteins in a variety of fundamental processes: photosynthesis, hydroxylation and nitrogen fixation to name but a few.The single-iron proteins in this class, the rubredoxins, have been studied extensively by chemical, spectroscopic and X-ray crystallographic techniques (Lovenberg, 1973), and the active site is composed of a single iron atom bound in a distorted tetrahedron of cysteine sulphur ligands. The iron is high-spin ferric in the oxidized state and high-spin ferrous in the reduced state. This structure is shown in Fig. I (α).

X-ray absorption spectroscopic studies of the high-spin iron(II) active site of isopenicillin N synthase: evidence for iron-sulfur interaction in the enzyme-substrate complex

Biochemistry ◽  
1992 ◽  
Vol 31 (19) ◽  
pp. 4596-4601 ◽  
Author(s):  
Robert A. Scott ◽  
Shengke Wang ◽  
Marly K. Eidsness ◽  
Aidas Kriauciunas ◽  
Charles A. Frolik ◽  
...  
Keyword(s):  
High Spin ◽  
Active Site ◽  
Spectroscopic Studies ◽  
X Ray ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Iron Sulfur ◽  
X Ray Absorption ◽  
Isopenicillin N ◽  
High Spin Iron

scholarly journals Electrochemical insights into the mechanism of NiFe membrane-bound hydrogenases

2016 ◽  
Vol 44 (1) ◽  
pp. 315-328 ◽  
Author(s):  
Lindsey A. Flanagan ◽  
Alison Parkin
Keyword(s):  
Active Site ◽  
Precious Metal ◽  
Active Sites ◽  
Review Paper ◽  
Spectroscopic Studies ◽  
Electrochemical Studies ◽  
Control Centre ◽  
Catalytic Active Sites ◽  
Membrane Bound ◽  
Insight Into

Hydrogenases are enzymes of great biotechnological relevance because they catalyse the interconversion of H2, water (protons) and electricity using non-precious metal catalytic active sites. Electrochemical studies into the reactivity of NiFe membrane-bound hydrogenases (MBH) have provided a particularly detailed insight into the reactivity and mechanism of this group of enzymes. Significantly, the control centre for enabling O2 tolerance has been revealed as the electron-transfer relay of FeS clusters, rather than the NiFe bimetallic active site. The present review paper will discuss how electrochemistry results have complemented those obtained from structural and spectroscopic studies, to present a complete picture of our current understanding of NiFe MBH.

scholarly journals An Overview of the Proofreading Functions in Bacteria and in Severe Acute Respiratory Syndrome-Coronaviruses

2021 ◽  
pp. 33-62
Author(s):  
Peramachi Palanivelu
Keyword(s):  
Amino Acids ◽  
Severe Acute Respiratory Syndrome ◽  
Structure Function ◽  
Active Site ◽  
Active Sites ◽  
Dna Polymerases ◽  
Proton Acceptor ◽  
Conserved Motifs ◽  
Bacterial Dna ◽  
X Ray

Aim: To understand the structure-function relationship of the proofreading (PR) functions in eubacteria and viruses with special reference to Severe Acute Respiratory Syndrome-Coronaviruses (SARS-CoVs) and propose a plausible mechanism of action for PR exonucleases of SARS-CoVs. Study Design: Bioinformatics, biochemical, site-directed mutagenesis (SDM), X-ray crystallographic data were used to study the structure-function relationships of the PR exonucleases from bacteria and CoVs. Methodology: The protein sequences of the PR exonucleases of various DNA polymerases, and RNA polymerases of SARS, SARS-related and human CoVs (HCoVs) were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available by biochemical, SDM experiments and X-ray crystallographic analysis on these enzymes were used to arrive at the possible active amino acids in the PR exonucleases of these crucial enzymes. Results:  A complete analysis of the active sites of the PR exonucleases from various bacteria and CoVs were done. The multiple sequence alignment (MSA) analysis showed many conserved amino acids, small and large peptide regions among them. Based on the conserved motifs, the PR exonucleases are found to fit broadly into two superfamilies, viz. DEDD and polymerase-histidinol phosphatase (PHP) superfamilies. The bacterial DNA polymerases I and II, RNase D, RNase T and ε-subunit of DNA polymerases III belong to the DEDD superfamily. The PR enzymes from SARS, SARS-related CoVs and other HCoVs also essentially belong to the DEDD superfamily. The DEDD superfamily either uses an invariant Tyr or a His as proton acceptor during catalysis. Depending on the proton acceptor, they are further classified into DEDHD and DEDYD subfamilies. RNase T, ε-subunit of DNA polymerases III and the SARS, SARS-related CoVs and other HCoVs belong to DEDHD subfamily.  However, the SARS, SARS-related CoVs and other HCoVs showed additional zinc finger motifs (ZFMs) in their active sites. DNA polymerases I, II and RNase D belong to DEDYD subfamily. The bacterial DNA polymerases X, YcdX phosphoesterases and the co-editing exonuclease of DNA polymerases III belong to the PHP superfamily. Based on the MSA, X-ray crystallographic analyses and SDM experiments, the proposed active-site proton acceptor is Tyr/His in DEDDY/H subfamilies and His in PHP superfamily of PR exonucleases.  Conclusions:   Based on the similarities of active site amino acids/motifs, it may be concluded that the DEDD and PHP superfamilies of PR exonucleases should have evolved from a common ancestor but diverged very long ago. The biochemical properties of these enzymes, including the four conserved acidic amino acid residues in the catalytic core, suggest that the CoVs might have acquired the exonuclease function, possibly from a prokaryote. However, the presence of two zinc fingers in the PR active site of the SARS, SARS-related CoVs and other HCoVs sets their PR exonucleases apart from other homologues.

scholarly journals A Cobalt-Iron Double-Atom Catalyst for the Oxygen Evolution Reaction

2019 ◽  
Author(s):  
Lichen Bai ◽  
Chia-Shuo Hsu ◽  
Duncan Alexander ◽  
Hao Ming Chen ◽  
Xile Hu
Keyword(s):  
Oxygen Evolution ◽  
Active Site ◽  
Oxygen Evolution Reaction ◽  
Active Sites ◽  
Single Atom ◽  
X Ray ◽  
Highly Active ◽  
Cobalt Iron ◽  
X Ray Absorption

Single atom catalysts exhibit well-defined active sites and potentially maximum atomic efficiency. However, they are unsuitable for reactions that benefit from bimetallic promotion such as the oxygen evolution reaction (OER) in alkaline medium. Here we show that a single atom Co precatalyst can be in-situ transformed into a Co-Fe double atom catalyst for OER. This catalyst exhibits one of the highest turnover frequencies among metal oxides. Electrochemical, microscopic, and spectroscopic data including those from operando X-ray absorption spectroscopy, reveal a dimeric Co-Fe moiety as the active site of the catalyst. This work demonstrates double-atom catalysis as a promising approach for the developed of defined and highly active OER catalysts.

scholarly journals In situ X-ray absorption spectroscopic studies of TiO2 photocatalytic active sites for degradation of trace CHCl3 in drinking water

2021 ◽  
Vol 28 (6) ◽  
Author(s):  
T.-L. Hsiung ◽  
L.-W. Wei ◽  
H.-L. Huang ◽  
H. Paul Wang
Keyword(s):  
Drinking Water ◽  
Photocatalytic Degradation ◽  
Active Sites ◽  
Spectroscopic Studies ◽  
Band Gap Energy ◽  
Disinfection Byproducts ◽  
Edge Structure ◽  
X Ray ◽  
X Ray Absorption

Toxic disinfection byproducts such as trihalomethanes (e.g. CHCl3) are often found after chlorination of drinking water. It has been found that photocatalytic degradation of trace CHCl3 in drinking water generally lacks an expected relationship with the crystalline phase, band-gap energy or the particle sizes of the TiO2-based photocatalysts used such as nano TiO2 on SBA-15 (Santa Barbara amorphous-15), TiO2 clusters (TiO2–SiO2) and atomic dispersed Ti [Ti-MCM-41 (Mobil Composition of Matter)]. To engineer capable TiO2 photocatalysts, a better understanding of their photoactive sites is of great importance and interest. Using in situ X-ray absorption near-edge structure (XANES) spectroscopy, the A1 (4969 eV), A2 (4971 eV) and A3 (4972 eV) sites in TiO2 can be distinguished as four-, five- and six- coordinated Ti species, respectively. Notably, the A2 Ti sites that are the main photocatalytic species of TiO2 are shown to be accountable for about 95% of the photocatalytic degradation of trace CHCl3 in drinking water (7.2 p.p.m. CHCl3 gTiO2 −1 h−1). This work reveals that the A2 Ti species of a TiO2-based photocatalyst are mainly responsible for the photocatalytic reactivity, especially in photocatalytic degradation of CHCl3 in drinking water.

X-ray absorption spectroscopic studies of the Fe(II) active site of catechol 2,3-dioxygenase. Implications for the extradiol cleavage mechanism

Biochemistry ◽  
1995 ◽  
Vol 34 (20) ◽  
pp. 6649-6659 ◽  
Author(s):  
Lijin Shu ◽  
Yu-Min Chiou ◽  
Allen M. Orville ◽  
Marcia A. Miller ◽  
John D. Lipscomb ◽  
...  
Keyword(s):  
Active Site ◽  
Spectroscopic Studies ◽  
X Ray ◽  
X Ray Absorption

scholarly journals Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray–derived conformational ensembles

2020 ◽  
Vol 117 (52) ◽  
pp. 33204-33215
Author(s):  
Filip Yabukarski ◽  
Justin T. Biel ◽  
Margaux M. Pinney ◽  
Tzanko Doukov ◽  
Alexander S. Powers ◽  
...  
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Enzyme Design ◽  
Reaction Cycle ◽  
New Era ◽  
X Ray ◽  
Enzyme Active Site ◽  
Conformational Ensembles ◽  
X Ray Crystallography ◽  
General Base

How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme’s reaction cycle. To examine positioning and motions and test catalytic proposals, we collected “room temperature” X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI’s reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI’s general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure–function relationships, providing the basis for a new era of “ensemble–function” interrogation of enzymes.

scholarly journals Palladium-doped hierarchical ZSM-5 for catalytic selective oxidation of allylic and benzylic alcohols

2021 ◽  
Vol 8 (10) ◽  
Author(s):  
Shengzhe Ding ◽  
Muhammad Ganesh ◽  
Yilai Jiao ◽  
Xiaoxia Ou ◽  
Mark A. Isaacs ◽  
...  
Keyword(s):  
Selective Oxidation ◽  
Active Site ◽  
Photoelectron Spectroscopy ◽  
Active Sites ◽  
Hierarchical Zeolites ◽  
X Ray ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Temperature Programmed ◽  
Alcohol Conversion

Hierarchical zeolites have the potential to provide a breakthrough in transport limitation, which hinders pristine microporous zeolites and thus may broaden their range of applications. We have explored the use of Pd-doped hierarchical ZSM-5 zeolites for aerobic selective oxidation (selox) of cinnamyl alcohol and benzyl alcohol to their corresponding aldehydes. Hierarchical ZSM-5 with differing acidity (H-form and Na-form) were employed and compared with two microporous ZSM-5 equivalents. Characterization of the four catalysts by X-ray diffraction, nitrogen porosimetry, NH 3 temperature-programmed desorption, CO chemisorption, high-resolution scanning transmission electron microscopy, X-ray photoelectron spectroscopy and X-ray absorption spectroscopy allowed investigation of their porosity, acidity, as well as Pd active sites. The incorporation of complementary mesoporosity, within the hierarchical zeolites, enhances both active site dispersion and PdO active site generation. Likewise, alcohol conversion was also improved with the presence of secondary mesoporosity, while strong Brønsted acidity, present solely within the H-form systems, negatively impacted overall selectivity through undesirable self-etherification. Therefore, tuning support porosity and acidity alongside active site dispersion is paramount for optimal aldehyde production.

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